Compositions and methods related to nucleic acid synthesis

ABSTRACT

The invention relates to the use of specific terminal deoxynucleotidyl transferase (TdT) enzymes in a method of nucleic acid synthesis, to methods of synthesizing nucleic acids, and to the use of kits comprising said enzymes in a method of nucleic acid synthesis. The invention also relates to the use of terminal deoxynucleotidyl transferases and 3′-blocked nucleotide triphosphates in a method of template independent nucleic acid synthesis.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/923,656 filed Jul. 8, 2020, which is a continuation of U.S. patentapplication Ser. No. 15/549,602, filed Aug. 8, 2017, which is a U.S.national phase application, pursuant to 35 U.S.C. 371, of PCTInternational Application No. PCT/GB2016/050301, filed Feb. 10, 2016.This international application claims priority to Great Britain PatentApplication No. 1502152.0, filed Feb. 10, 2015. The contents of theaforementioned patent applications are incorporated herein by referencein their entireties.

SEQUENCE LISTING

A computer readable text file, entitled “SequenceListing.txt,” createdon or about Jul. 8, 2020 with a file size of about 32,768 bytes containsthe sequence listing for this application and is hereby incorporated byreference in its entirety.

FIELD OF THE INVENTION

The invention relates to the use of specific terminal deoxynucleotidyltransferase (TdT) enzymes in a method of nucleic acid synthesis, tomethods of synthesizing nucleic acids, and to the use of kits comprisingsaid enzymes in a method of nucleic acid synthesis. The invention alsorelates to the use of terminal deoxynucleotidyl transferases and3′-blocked nucleotide triphosphates in a method of template independentnucleic acid synthesis.

BACKGROUND OF THE INVENTION

Nucleic acid synthesis is vital to modern biotechnology. The rapid paceof development in the biotechnology arena has been made possible by thescientific community's ability to artificially synthesise DNA, RNA andproteins.

Artificial DNA synthesis—a £1 billion and growing market—allowsbiotechnology and pharmaceutical companies to develop a range of peptidetherapeutics, such as insulin for the treatment of diabetes. It allowsresearchers to characterise cellular proteins to develop new smallmolecule therapies for the treatment of diseases our aging populationfaces today, such as heart disease and cancer. It even paves the wayforward to creating life, as the Venter Institute demonstrated in 2010when they placed an artificially synthesised genome into a bacterialcell.

However, current DNA synthesis technology does not meet the demands ofthe biotechnology industry. While the benefits of DNA synthesis arenumerous, an oft-mentioned problem prevents the further growth of theartificial DNA synthesis industry, and thus the biotechnology field.Despite being a mature technology, it is practically impossible tosynthesise a DNA strand greater than 200 nucleotides in length, and mostDNA synthesis companies only offer up to 120 nucleotides. In comparison,an average protein-coding gene is of the order of 2000-3000 nucleotides,and an average eukaryotic genome numbers in the billions of nucleotides.Thus, all major gene synthesis companies today rely on variations of a‘synthesise and stitch’ technique, where overlapping 40-60-mer fragmentsare synthesised and stitched together by PCR (see Young, L. et al.(2004) Nucleic Acid Res. 32, e59). Current methods offered by the genesynthesis industry generally allow up to 3 kb in length for routineproduction.

The reason DNA cannot be synthesised beyond 120-200 nucleotides at atime is due to the current methodology for generating DNA, which usessynthetic chemistry (i.e., phosphoramidite technology) to couple anucleotide one at a time to make DNA. As the efficiency of eachnucleotide-coupling step is 95.0-99.5% efficient, it is mathematicallyimpossible to synthesise DNA longer than 200 nucleotides in acceptableyields. The Venter Institute illustrated this laborious process byspending 4 years and 20 million USD to synthesise the relatively smallgenome of a bacterium (see Gibson, D. G. et al. (2010) Science 329,52-56).

Known methods of DNA sequencing use template-dependent DNA polymerasesto add 3′-reversibly terminated nucleotides to a growing double-strandedsubstrate (see, Bentley, D. R. et al. (2008) Nature 456, 53-59). In the‘sequencing-by-synthesis’ process, each added nucleotide contains a dye,allowing the user to identify the exact sequence of the template strand.Albeit on double-stranded DNA, this technology is able to producestrands of between 500-1000 bps long. However, this technology is notsuitable for de novo nucleic acid synthesis because of the requirementfor an existing nucleic acid strand to act as a template.

Various attempts have been made to use a terminal deoxynucleotidyltransferase for controlled de novo single-stranded DNA synthesis (seeUd-Dean, S. M. M. (2009) Syst Synth Boil 2, 67-73, U.S. Pat. Nos.5,763,594 and 8,808,989). Uncontrolled de novo single-stranded DNAsynthesis, as opposed to controlled, takes advantage of TdT'sdeoxynucleotide triphosphate (dNTP) 3′ tailing properties onsingle-stranded DNA to create, for example, homopolymeric adaptorsequences for next-generation sequencing library preparation (seeRoychoudhury R., et al. (1976) Nucleic Acids Res 3, 101-116 and WO2003/050242). A reversible deoxynucleotide triphosphate terminationtechnology needs to be employed to prevent uncontrolled addition ofdNTPs to the 3′-end of a growing DNA strand. The development of acontrolled single-stranded DNA synthesis process through TdT would beinvaluable to in situ DNA synthesis for gene assembly or hybridizationmicroarrays as it removes the need for an anhydrous environment andallows the use of various polymers incompatible with organic solvents(see Blanchard, A. P. (1996) Biosens Bioelectron 11, 687-690 and U.S.Pat. No. 7,534,561).

However, TdT has not been shown to efficiently add nucleotidetriphosphates containing 3′-O reversibly terminating moieties forbuilding up a nascent single-stranded DNA chain necessary for a de novosynthesis cycle. A 3′-O reversible terminating moiety would prevent aterminal transferase like TdT from catalysing the nucleotide transferasereaction between the 3′-end of a growing DNA strand and the5′-triphosphate of an incoming nucleotide triphosphate. Data ispresented herein which demonstrates that the widely commerciallyavailable recombinant TdT sourced from calf thymus is unable to add3′-O-terminated nucleotide triphosphates in a quantitative fashion (seeFIG. 3 ). In previous reports, the TdT specifically mentioned isrecombinant TdT from calf thymus (see Ud-Dean, S. M. M. (2009) SystSynth Boil 2, 67-73, U.S. Pat. Nos. 5,763,594 and 8,808,989) or uses adifferent reversible terminating mechanism not located on the 3′ end ofthe deoxyribose moiety (see U.S. Pat. No. 8,808,989).

Most DNA and RNA polymerases contain highly selective sugar steric gatesto tightly discriminate between deoxyribose and ribose nucleotidetriphosphate substrates (see Joyce C. M. (1997) Proc Natl Acad Sci 94,1619-22). The result of this sugar steric gate is the enormous challengeof finding and/or engineering polymerases to accept sugar variants forbiotechnology reasons, such as sequencing-by-synthesis (see Metzker M.L. (2010) Nat Rev Genet 11, 31-46 and U.S. Pat. No. 8,460,910). Thechallenge of finding a polymerase that accepts a 3′-O reversiblyterminating nucleotide is so large, various efforts have been made tocreate reversible terminating nucleotides where the polymerasetermination mechanism is located on the nitrogenous base of theterminating nucleotide (see Gardner, A. F. (2012) Nucleic Acids Res 40,7404-15 and U.S. Pat. No. 8,889,860).

There is therefore a need to identify terminal deoxynucleotidyltransferases that readily incorporate 3′-O reversibly terminatednucleotides and modified said terminal deoxynucleotidyl transferases toincorporate 3′-O reversibly terminated nucleotides in a fashion usefulfor biotechnology and single-stranded DNA synthesis processes in orderto provide an improved method of nucleic acid synthesis that is able toovercome the problems associated with currently available methods.

SUMMARY OF THE INVENTION

According to a first aspect of the invention, there is provided the useof a terminal deoxynucleotidyl transferase (TdT) enzyme comprising anamino acid sequence selected from either: (a) any one of SEQ ID NOS: 1to 5 and 8 or a functional equivalent or fragment thereof having atleast 20% sequence homology to said amino acid sequence; or (b) amodified derivative of SEQ ID NO: 6; in a method of nucleic acidsynthesis.

According to a second aspect of the invention, there is provided amethod of nucleic acid synthesis, which comprises the steps of:

-   -   (a) providing an initiator sequence;    -   (b) adding a 3′-blocked nucleotide triphosphate to said        initiator sequence in the presence of a terminal        deoxynucleotidyl transferase (TdT) as defined in the first        aspect of the invention;    -   (c) removal of all reagents from the initiator sequence;    -   (d) cleaving the blocking group from the 3′-blocked nucleotide        triphosphate in the presence of a cleaving agent;    -   (e) removal of the cleaving agent.

According to a further aspect of the invention, there is provided theuse of a kit in a method of nucleic acid synthesis, wherein said kitcomprises a TdT as defined in the first or second aspects of theinvention optionally in combination with one or more components selectedfrom: an initiator sequence, one or more 3′-blocked nucleotidetriphosphates, inorganic pyrophosphatase, such as purified, recombinantinorganic pyrophosphatase from Saccharomyces cerevisiae, and a cleavingagent; further optionally together with instructions for use of the kitin accordance with any of the methods defined herein.

According to a further aspect of the invention, there is provided theuse of a 3′-blocked nucleotide triphosphate in a method of templateindependent nucleic acid synthesis, wherein the 3′-blocked nucleotidetriphosphate is selected from a compound of formula (I), (II), (III) or(IV):

wherein

-   -   R¹ represents NR^(a)R^(b), wherein R^(a) and R^(b) independently        represent hydrogen or C₁₋₆ alkyl,    -   R² represents hydrogen, C₁₋₆ alkyl, C₁₋₆ alkoxy, COH or COOH.    -   X represents C₁₋₆ alkyl, NH₂, N₃ or —OR³,    -   R³ represents C₁₋₆ alkyl, CH₂N₃, NH₂ or allyl,    -   Y represents hydrogen, halogen or hydroxyl, and    -   Z represents CR⁴ or N, wherein R⁴ represents hydrogen, C₁₋₆        alkyl, C₁₋₆alkoxy, COH or COOH.

According to a further aspect of the invention, there is provided theuse of inorganic pyrophosphatase in a method of nucleic acid synthesis.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 : Schematic of enzymatic DNA synthesis process. Starting from thetop of the diagram, an immobilised strand of DNA with a deprotected3′-end is exposed to an extension mixture composed of TdT, abase-specific 3′-blocked nucleotide triphosphate, inorganicpyrophosphatase to reduce the buildup of inorganic pyrophosphate, andappropriate buffers/salts for optimal enzyme activity and stability. Theprotein adds one protected nucleotide to the immobilised DNA strand(bottom of diagram). The extension mixture is then removed with washmixture and optionally recycled. The immobilised (n+1) DNA strand isthen washed with a cleavage mixture to cleave the 3′-protecting group,enabling reaction in the next cycle. In the cleavage mixture, denaturantmay be present to disrupt any secondary structures. During this step,the temperature may be raised to assist in cleavage and disruption ofsecondary structures. The immobilised DNA is treated with wash mixtureto remove leftover cleavage mixture. Steps 1˜4 may be repeated with anappropriate nucleotide triphosphate until the desired oligonucleotidesequence is achieved.

FIG. 2 : TdT adds a 3′-irreversibly blocked nucleotide triphosphate toan initiator strand. (A) A single-stranded DNA initiator was incubatedwith 15 U Bos taurus TdT, required salts (50 mM potassium acetate, 20 mMtris acetate pH 7.9, 1 mM cobalt chloride), and 3′-O-Methyl dTTP at 37°C. for the indicated amount of time. The 3′-irreversibly blockednucleotide triphosphate was at a concentration of 1 mM and the DNAinitiator at 200 pM for a 1:5000 ratio to encourage nucleotide addition.The reaction was stopped with EDTA (0.5 M). (B) Similar to (A) with theexception that 3′-Azido dTTP was used as the 3′-blocked nucleotidetriphosphate.

FIG. 3 : Various TdT orthologs add a 3′-reversibly protected(3′-O-azidomethyl) nucleotide triphosphate to an initiator strand up to3.8-fold faster than Bos taurus TdT. (A) A single-stranded DNA initiatorwas incubated with TdT with the indicated species for 60 min in theabove mentioned buffer and reaction conditions. Reactions were thenanalysed by capillary electrophoresis and a subset of chromatograms areshown. (B) Fraction of DNA initiator strand converted to N+1 species(addition of 3′-O-azidomethyl dTTP) in one hour. (C) Three TdT orthologswere reacted with 3′-O-azidomethyl dTTP and 3′-O-azidomethyl dCTP for 20min. Lepisosteus oculatus and Sarcophilus harrisii TdT consistentlyperform better compared to Bos taurus TdT. The ability for TdT orthologsto add both dTTP and dCTP nucleotide analogs demonstrate control of DNAsequence specificity.

FIG. 4 : An engineered variant of Lepisosteus oculatus TdT showsimproved activity over the wild-type Lepisosteus oculatus TdT. A DNAinitiator strand was incubated with 1 mM 3′-reversibly blocked dNTP at37° C. for 20 minutes with required salts as described previously.Addition of the dNTP was measured by PAGE and the conversion relative towild-type TdT was plotted.

FIG. 5 : An engineered variant of Lepisosteus oculatus shows vastlyimproved activity over the wild-type TdT (see FIG. 3 ) and commerciallyavailable Bos taurus TdT. TdT was incubated with a DNA initiator and a3′-reversibly blocked dNTP in a similar fashion as previously described.Bos taurus TdT was outperformed by an engineered variant of Lepisosteusoculatus TdT, as demonstrated in the PAGE gel.

FIG. 6 : Inorganic pyrophosphate is necessary for TdT-mediated, de novosequence specific DNA synthesis. A nucleic acid initiator was incubatedwith and without Saccharomyces cerevisiae inorganic pyrophosphatase andBos taurus TdT at 37° C. in 50 mM potassium acetate, 20 mM tris acetatepH 7.9, 1.5 mM cobalt chloride. 3′-O-azidomethyl dTTP (N₃Me-dTTP) wasintroduced at 1 mM and dideoxyTTP (ddTTP) was introduced at 100 μM. Thereactions were analysed by PAGE. Without inorganic pyrophosphatase,strand dismutation predominates and catastrophic loss ofsequence-specificity occurs.

FIG. 7 : Simplified schematic representation of a column-based flowinstrument used in DNA synthesis. A computer (302) controls two pumpsand a solution mixing chamber (311). Pump 1 (304) selectively pumpsextension solution (301), wash solution (305) or cleavage solution (310)into the mixing chamber. Pump 2 (306) selectively pumps a single3′-blocked nucleotide triphosphate (TP) solution containing either3′-blocked A(adenine)TP (303), T(thymine)TP (307), G(guanine)TP (308),or C(cytosine)TP (309) into the chamber. The computer controlled mixingchamber then passes appropriate solution ratios from pump 1 and pump 2into a column based DNA synthesis chamber (312). A heating element (313)ensures that the DNA synthesis column remains at the necessarytemperature for the synthesis process to take place. Upon exiting theDNA synthesis chamber, the reaction solution either enters a recyclingvessel (314) for future use, a waste vessel (316) or moves on to apolymerase chain reaction (PCR) step (315) for amplification of theresultant DNA. PCR completion leads to the final product (317).

DETAILED DESCRIPTION OF THE INVENTION

According to a first aspect of the invention, there is provided the useof a terminal deoxynucleotidyl transferase (TdT) enzyme comprising anamino acid sequence selected from either: (a) any one of SEQ ID NOS: 1to 5 and 8 or a functional equivalent or fragment thereof having atleast 20% sequence homology to said amino acid sequence; or (b) amodified derivative of SEQ ID NO: 6; in a method of nucleic acidsynthesis.

According to one particular aspect of the invention which may bementioned, there is provided the use of a terminal deoxynucleotidyltransferase (TdT) enzyme comprising an amino acid sequence selected fromeither: (a) any one of SEQ ID NOS: 1 to 5 or a functional equivalent orfragment thereof having at least 20% sequence homology to said aminoacid sequence; or (b) a modified derivative of SEQ ID NO: 6; in a methodof nucleic acid synthesis.

The present invention relates to the identification of never beforestudied terminal deoxynucleotidyl transferases that surprisingly havethe ability to incorporate deoxynucleotide triphosphates with large 3′-Oreversibly terminating moieties.

Since commercially available recombinant TdT sourced from calf thymusdoes not readily incorporate 3′-O reversibly terminated nucleotides, itis most unexpected that the present inventors have located a terminaldeoxynucleotidyl transferase, which is a DNA polymerase, to accept a3′-O reversibly terminating nucleotide, such as dNTPs modified with a3′-O-azidomethyl.

Furthermore, the present invention relates to engineered terminaldeoxynucleotidyl transferases, which achieve a substantial increase inincorporation rates of dNTPs containing 3′-O reversibly terminatingmoieties to be useful for the controlled de novo synthesis ofsingle-stranded DNA.

As controlled de novo single-stranded DNA synthesis is an additiveprocess, coupling efficiency is extremely important to obtainingpractically useful yields of final single-stranded DNA product for usein applications such as gene assembly or hybridization microarrays.Thus, the present invention relates to the identification of TdTorthologs with the capability to add 3′-O reversibly terminatednucleotides, and also an engineered variant of the TdT ortholog thatadds 3′-O reversibly terminated nucleotides in a quantitative fashionthat is practically useful for a single-stranded DNA synthesis process.

The use described herein has significant advantages, such as the abilityto rapidly produce long lengths of DNA while still maintaining highyields and without using any toxic organic solvents.

In one embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from any one of SEQ IDNOS: 1 to 5 and 8 or a functional equivalent or fragment thereof havingat least 20% sequence homology to said amino acid sequence.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from any one of SEQ IDNOS: 1 to 5 or a functional equivalent or fragment thereof having atleast 20% sequence homology to said amino acid sequence.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 1. Theamino acid sequence of SEQ ID NO: 1 is the terminal deoxynucleotidyltransferase (TdT) sequence from Sarcophilus harrisii (UniProt: G3VQ55).Sarcophilus harrisii (also known as the Tasmanian devil) is acarnivorous marsupial of the family Dasyuridae, now found in the wildonly on the Australian island state of Tasmania.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 2. Theamino acid sequence of SEQ ID NO: 2 is the terminal deoxynucleotidyltransferase (TdT) sequence from Lepisosteus oculatus (UniProt: W5MK82).Lepisosteus oculatus (also known as the spotted gar) is a primitivefreshwater fish of the family Lepisosteidae, native to North Americafrom the Lake Erie and southern Lake Michigan drainages south throughthe Mississippi River basin to Gulf Slope drainages, from lowerApalachicola River in Florida to Nueces River in Texas, USA.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 3. Theamino acid sequence of SEQ ID NO: 3 is the terminal deoxynucleotidyltransferase (TdT) sequence from Chinchilla lanigera (NCBI ReferenceSequence: XP_005407631.1;http://www.ncbi.nim.nih.gov/protein/533189443). Chinchilla lanigera(also known as the long-tailed chinchilla, Chilean, coastal, commonchinchilla, or lesser chinchilla), is one of two species of rodents fromthe genus Chinchilla, the other species being Chinchilla chinchilla.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 4. Theamino acid sequence of SEQ ID NO: 4 is the terminal deoxynucleotidyltransferase (TdT) sequence from Otolemur garnettii (UniProt: A4PCE6).Otolemur garnettii (also known as the northern greater galago, Garnett'sgreater galago or small-eared greater galago), is a nocturnal, arborealprimate endemic to Africa.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 5. Theamino acid sequence of SEQ ID NO: 5 is the terminal deoxynucleotidyltransferase (TdT) sequence from Sus scrofa (UniProt: F1SBG2). Sus scrofa(also known as the wild boar, wild swine or Eurasian wild pig) is a suidnative to much of Eurasia, North Africa and the Greater Sunda Islands.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 8. Theamino acid sequence of SEQ ID NO: 8 is a variant of SEQ ID NO: 2 whichhas been engineered for improved activity by alteration of the aminoacid sequence. Data are provided in Example 3 and FIG. 4 , whichdemonstrate the benefits of engineered variants, such as SEQ ID NO: 8,over the wild-type SEQ ID NO: 2.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NOS: 1, 2or 8.

In a further embodiment, the terminal deoxynucleotidyl transferase (TdT)enzyme comprises an amino acid sequence selected from SEQ ID NO: 1 or 2.Data are provided in Example 2 and FIG. 3 , which demonstrate beneficialresults over the natural, recombinant TdT enzyme from Bos taurus.

In an alternative embodiment, the terminal deoxynucleotidyl transferase(TdT) enzyme comprises an amino acid sequence selected from a modifiedderivative of SEQ ID NO: 6 (i.e. a non-natural, mutated derivative ofSEQ ID NO: 6). The amino acid sequence of SEQ ID NO: 6 is the terminaldeoxynucleotidyl transferase (TdT) sequence from Bos taurus (UniProt:P06526). Bos taurus (also known as cattle, or colloquially cows) are themost common type of large domesticated ungulates. They are a prominentmodern member of the subfamily Bovinae, are the most widespread speciesof the genus Bos.

References herein to “TdT” refer to a terminal deoxynucleotidyltransferase (TdT) enzyme and include references to purified andrecombinant forms of said enzyme. TdT Is also commonly known as DNTT(DNA nucleotidylexotransferase) and any such terms should be usedinterchangeably.

References herein to a “method of nucleic acid synthesis” includemethods of synthesising lengths of DNA (deoxyribonucleic acid) or RNA(ribonucleic acid) wherein a strand of nucleic acid (n) is extended byadding a further nucleotide (n+1). In one embodiment, the nucleic acidis DNA. In an alternative embodiment, the nucleic acid is RNA.

References herein to “method of DNA synthesis” refer to a method of DNAstrand synthesis wherein a DNA strand (n) is extended by adding afurther nucleotide (n+1). The method described herein provides a noveluse of the terminal deoxynucleotidyl transferases of the invention and3′-reversibly blocked nucleotide triphosphates to sequentially addnucleotides in de novo DNA strand synthesis which has several advantagesover the DNA synthesis methods currently known in the art.

Current synthetic methods for coupling nucleotides to formsequence-specific DNA have reached asymptotic length limits, therefore anew method of de novo DNA synthesis is required. Synthetic DNA synthesismethods also have the disadvantage of using toxic organic solvents andadditives (e.g., acetonitrile, acetic anhydride, trichloroacetic acid,pyridine, etc.), which are harmful to the environment.

An alternative, enzymatic method of nucleic acid synthesis is desirable.Natural enzymes such as DNA polymerases are able to add 50,000nucleotides before disassociation. However, DNA polymerases require atemplate strand, thereby defeating the purpose of de novo strandsynthesis.

However, a DNA polymerase, called TdT, capable of template-independentDNA synthesis is found in vertebrates. Given a free 3′-end andnucleotide triphosphates, recombinant TdTs from Bos taurus and Musmusculus were shown to add ten to several hundred nucleotides onto the3′-end of a DNA strand. As shown in a paper by Basu, M. et al. (Biochem.Biophys. Res. Commun. (1983) 111, 1105-1112) TdT will uncontrollably addnucleotide triphosphates to the 3′-end of a DNA strand. However, thisuncontrolled addition is unsuitable for controlled de novo strandsynthesis where a sequence-specific oligonucleotide is required. Thus,commercially available recombinant TdT is used primarily as a tool formolecular biologists to label DNA with useful chemical tags.

The present inventors have discovered several orthologs of Bos taurusTdT that, coupled with 3′-reversibly protected nucleotide triphosphates,are able to synthesise DNA in a controlled manner. Bos taurus TdT is notefficient at incorporating nucleotide triphosphates with 3′-protectinggroups, likely due to steric issues in the TdT active site. Data ispresented herein in Example 2 and FIG. 3 which demonstrates thatorthologs of Bos taurus TdT, such as the purified recombinant TdTs ofthe first aspect of the invention (in particular SEQ ID NOS: 1 and 2),are far more efficient at incorporating 3′-OH blocked nucleotidetriphosphates, thereby enabling template-independent, sequence-specificsynthesis of nucleic acid strands.

This enzymatic approach means that the method has the particularadvantage of being able to produce DNA strands beyond the 120-200nucleotide limit of current synthetic DNA synthesis methods.Furthermore, this enzymatic method avoids the need to use strong organicsolvents which may be harmful to the environment.

It will be understood that the term ‘functional equivalent’ refers tothe polypeptides which are different to the exact sequence of the TdTsof the first aspect of the invention, but can perform the same function,i.e., catalyse the addition of a nucleotide triphosphate onto the 3′-endof a DNA strand in a template dependent manner.

In one embodiment, the terminal deoxynucleotidyl transferase (TdT) is anon-natural derivative of TdT, such as a functional fragment or homologof the TdTs of the first aspect of the invention.

References herein to ‘fragment’ include, for example, functionalfragments with a C-terminal truncation, or with an N-terminaltruncation. Fragments are suitably greater than 10 amino acids inlength, for example greater than 15, 20, 25, 30, 35, 40, 45, 50, 55, 60,65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180,190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320,330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460,470, 480, 490 or 500 amino acids in length.

It will be appreciated that references herein to “homology” are to beunderstood as meaning the percentage identity between two proteinsequences, e.g.: SEQ ID NO: X and SEQ ID NO: Y, which is the sum of thecommon amino acids between aligned sequences SEQ ID NO: X and SEQ ID NO:Y, divided by the shorter length of either SEQ ID NO: X or SEQ ID NO: Y,expressed as a percentage.

In one embodiment, the terminal deoxynucleotidyl transferase (TdT) hasat least 25% homology with the TdTs of the first aspect of theinvention, such as at least 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 96%, 97%, 98% or 99% homology.

According to a second aspect of the invention, there is provided amethod of nucleic acid synthesis, which comprises the steps of:

-   -   (a) providing an initiator sequence;    -   (b) adding a 3′-blocked nucleotide triphosphate to said        initiator sequence in the presence of a terminal        deoxynucleotidyl transferase (TdT) as defined in the first        aspect of the invention;    -   (c) removal of all reagents from the initiator sequence;    -   (d) cleaving the blocking group from the 3′-blocked nucleotide        triphosphate in the presence of a cleaving agent;    -   (e) removal of the cleaving agent.

In one embodiment, step (c) comprises removal of deoxynucleotidetriphosphates and TdT, such as TdT. Thus, according to one particularaspect of the invention, there is provided a method of nucleic acidsynthesis, which comprises the steps of:

-   -   (a) providing an initiator sequence;    -   (b) adding a 3′-blocked nucleotide triphosphate to said        initiator sequence in the presence of a terminal        deoxynucleotidyl transferase (TdT) as defined in the first        aspect of the invention;    -   (c) removal of TdT;    -   (d) cleaving the blocking group from the 3′-blocked nucleotide        triphosphate in the presence of a cleaving agent;    -   (e) removal of the cleaving agent.

It will be understood that steps (b) to (e) of the method may berepeated multiple times to produce a DNA or RNA strand of a desiredlength. Therefore, in one embodiment, greater than 1 nucleotide is addedto the initiator sequence, such as greater than 5, 10, 20, 30, 40, 50,60, 70, 80, 90, 100, 110 or 120 nucleotides are added to the initiatorsequence by repeating steps (b) to (e). In a further embodiment, greaterthan 200 nucleotides are added, such as greater than 300, 400, 500, 600,700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000,4000, 5000, 6000, 7000, 8000, 9000 or 10000 nucleotides.

3′-Blocked Nucleotide Triphosphates

References herein to ‘nucleotide triphosphates’ refer to a moleculecontaining a nucleoside (i.e. a base attached to a deoxyribose or ribosesugar molecule) bound to three phosphate groups. Examples of nucleotidetriphosphates that contain deoxyribose are: deoxyadenosine triphosphate(dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate(dCTP) or deoxythymidine triphosphate (dTTP). Examples of nucleotidetriphosphates that contain ribose are: adenosine triphosphate (ATP),guanosine triphosphate (GTP), cytidine triphosphate (CTP) or uridinetriphosphate (UTP). Other types of nucleosides may be bound to threephosphates to form nucleotide triphosphates, such as naturally occurringmodified nucleosides and artificial nucleosides.

Therefore, references herein to ‘3’-blocked nucleotide triphosphates'refer to nucleotide triphosphates (e.g., dATP, dGTP, dCTP or dTTP) whichhave an additional group on the 3′ end which prevents further additionof nucleotides, i.e., by replacing the 3′-OH group with a protectinggroup.

It will be understood that references herein to ‘3′-block’, ‘3′-blockinggroup’ or ‘3′-protecting group’ refer to the group attached to the 3′end of the nucleotide triphosphate which prevents further nucleotideaddition. The present method uses reversible 3′-blocking groups whichcan be removed by cleavage to allow the addition of further nucleotides.By contrast, irreversible 3′-blocking groups refer to dNTPs where the3′-OH group can neither be exposed nor uncovered by cleavage.

There exist several documented reversible protecting groups, such asazidomethyl, aminoxy, and allyl, which can be applied to the methoddescribed herein. Examples of suitable protecting groups are describedin Greene's Protective Groups in Organic Synthesis, (Wuts, P. G. M. &Greene, T. W. (2012) 4th Ed., John Wiley & Sons).

In one embodiment, the 3′-blocked nucleotide triphosphate is blocked bya reversible protecting group. In an alternative embodiment, the3′-blocked nucleotide triphosphate is blocked by an irreversibleprotecting group.

Therefore, in one embodiment, the 3′-blocked nucleotide triphosphate isblocked by either a 3′-O-methyl, 3′-azido, 3′-O-azidomethyl, 3′-aminoxyor 3′-O-allyl group. In a further embodiment, the 3′-blocked nucleotidetriphosphate is blocked by either a 3′-O-azidomethyl, 3′-aminoxy or3′-O-allyl group. In an alternative embodiment, the 3′-blockednucleotide triphosphate is blocked by either a 3′-O-methyl or 3′-azidogroup.

Cleaving Agent

References herein to ‘cleaving agent’ refer to a substance which is ableto cleave the 3′-blocking group from the 3′-blocked nucleotidetriphosphate.

The 3′-blocking groups described herein may all be quantitativelyremoved in aqueous solution with documented compounds which may be usedas cleaving agents (for example, see: Wuts, P. G. M. & Greene, T. W.(2012) 4th Ed., John Wiley & Sons; Hutter, D. et al. (2010) NucleosidesNucleotides Nucleic Acids 29, 879-895; EP 1560838 and U.S. Pat. No.7,795,424).

In one embodiment, the cleaving agent is a chemical cleaving agent. Inan alternative embodiment, the cleaving agent is an enzymatic cleavingagent.

It will be understood by the person skilled in the art that theselection of cleaving agent is dependent on the type of 3′-nucleotideblocking group used. For instance, tris(2-carboxyethyl)phosphine (TCEP)can be used to cleave a 3′-O-azidomethyl group, palladium complexes canbe used to cleave a 3′-O-allyl group, or sodium nitrite can be used tocleave a 3′-aminoxy group. Therefore, in one embodiment, the cleavingagent is selected from: tris(2-carboxyethyl)phosphine (TCEP), apalladium complex or sodium nitrite.

In one embodiment, the cleaving agent is added in the presence of acleavage solution comprising a denaturant, such as urea, guanidiniumchloride, formamide or betaine. The addition of a denaturant has theadvantage of being able to disrupt any undesirable secondary structuresin the DNA. In a further embodiment, the cleavage solution comprises oneor more buffers. It will be understood by the person skilled in the artthat the choice of buffer is dependent on the exact cleavage chemistryand cleaving agent required.

Initiator Sequences

References herein to an ‘initiator sequence’ refer to a shortoligonucleotide with a free 3′-end which the 3′-blocked nucleotidetriphosphate can be attached to. In one embodiment, the initiatorsequence is a DNA initiator sequence. In an alternative embodiment, theinitiator sequence is an RNA initiator sequence.

References herein to a ‘DNA initiator sequence’ refer to a smallsequence of DNA which the 3′-blocked nucleotide triphosphate can beattached to, i.e. DNA will be synthesised from the end of the DNAinitiator sequence.

In one embodiment, the initiator sequence is between 5 and 50nucleotides long, such as between 5 and 30 nucleotides long (i.e.between 10 and 30), in particular between 5 and 20 nucleotides long(i.e., approximately 20 nucleotides long), more particularly 5 to 15nucleotides long, for example 10 to 15 nucleotides long, especially 12nucleotides long.

In one embodiment, the initiator sequence has the following sequence:5′-CGTTAACATATT-3′ (SEQ ID NO: 7).

In one embodiment, the initiator sequence is single-stranded. In analternative embodiment, the initiator sequence is double-stranded. Itwill be understood by persons skilled in the art that a 3′-overhang(i.e., a free 3′-end) allows for efficient addition.

In one embodiment, the initiator sequence is immobilised on a solidsupport. This allows TdT and the cleaving agent to be removed (in steps(c) and (e), respectively) without washing away the synthesised nucleicacid. The initiator sequence may be attached to a solid support stableunder aqueous conditions so that the method can be easily performed viaa flow setup.

In one embodiment, the initiator sequence is immobilised on a solidsupport via a reversible interacting moiety, such as achemically-cleavable linker, an antibody/immunogenic epitope, abiotin/biotin binding protein (such as avidin or streptavidin), orglutathione-GST tag. Therefore, in a further embodiment, the methodadditionally comprises extracting the resultant nucleic acid by removingthe reversible interacting moiety in the initiator sequence, such as byincubating with proteinase K.

In a further embodiment, the initiator sequence is immobilised on asolid support via a chemically-cleavable linker, such as a disulfide,allyl, or azide-masked hemiaminal ether linker. Therefore, in oneembodiment, the method additionally comprises extracting the resultantnucleic acid by cleaving the chemical linker through the addition oftris(2-carboxyethyl)phosphine (TCEP) or dithiothreitol (DTT) for adisulfide linker; palladium complexes for an allyl linker; or TCEP foran azide-masked hemiaminal ether linker.

In one embodiment, the resultant nucleic acid is extracted and amplifiedby polymerase chain reaction using the nucleic acid bound to the solidsupport as a template. The initiator sequence could therefore contain anappropriate forward primer sequence and an appropriate reverse primercould be synthesised.

In an alternative embodiment, the immobilised initiator sequencecontains at least one restriction site. Therefore, in a furtherembodiment, the method additionally comprises extracting the resultantnucleic acid by using a restriction enzyme.

The use of restriction enzymes and restriction sites to cut nucleicacids in a specific location is well known in the art. The choice ofrestriction site and enzyme can depend on the desired properties, forexample whether ‘blunt’ or ‘sticky’ ends are required. Examples ofrestriction enzymes include: AluI, BamHI, EcoRI, EcoRII, EcoRV, HaeII,HgaI, HindIII, HinfI, NotI, PstI, PvuII, SaII, Sau3A, ScaI, SmaI, TaqIand XbaI.

In an alternative embodiment, the initiator sequence contains at leastone uridine. Treatment with uracil-DNA glycosylase (UDG) generates anabasic site. Treatment on an appropriate substrate with anapurinic/apyrimidinic (AP) site endonuclease will extract the nucleicacid strand.

Nucleic Acid Synthesis Method

In one embodiment, the terminal deoxynucleotidyl transferase (TdT) ofthe invention is added in the presence of an extension solutioncomprising one or more buffers (e.g., Tris or cacodylate), one or moresalts (e.g., Na⁺, K⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺, Co²⁺, etc., all withappropriate counterions, such as Cl⁻) and inorganic pyrophosphatase(e.g., the Saccharomyces cerevisiae homolog). It will be understood thatthe choice of buffers and salts depends on the optimal enzyme activityand stability.

The use of an inorganic pyrophosphatase helps to reduce the build-up ofpyrophosphate due to nucleotide triphosphate hydrolysis by TdT.Therefore, the use of an inorganic pyrophosphatase has the advantage ofreducing the rate of (1) backwards reaction and (2) TdT stranddismutation. Thus, according to a further aspect of the invention, thereis provided the use of inorganic pyrophosphatase in a method of nucleicacid synthesis. Data is presented herein in Example 5 and FIG. 6 whichdemonstrates the benefit of the use of inorganic pyrophosphatase duringnucleic acid synthesis. In one embodiment, the inorganic pyrophosphatasecomprises purified, recombinant inorganic pyrophosphatase fromSaccharomyces cerevisiae.

In one embodiment, step (b) is performed at a pH range between 5 and 10.Therefore, it will be understood that any buffer with a buffering rangeof pH 5-10 could be used, for example cacodylate, Tris, HEPES orTricine, in particular cacodylate or Tris.

In one embodiment, step (d) is performed at a temperature less than 99°C., such as less than 95° C., 90° C., 85° C., 80° C., 75° C., 70° C.,65° C., 60° C., 55° C., 50° C., 45° C., 40° C., 35° C., or 30° C. Itwill be understood that the optimal temperature will depend on thecleavage agent utilised. The temperature used helps to assist cleavageand disrupt any secondary structures formed during nucleotide addition.

In one embodiment, steps (c) and (e) are performed by applying a washsolution. In one embodiment, the wash solution comprises the samebuffers and salts as used in the extension solution described herein.This has the advantage of allowing the wash solution to be collectedafter step (c) and recycled as extension solution in step (b) when themethod steps are repeated.

In one embodiment, the method is performed within a flow instrument asshown in FIG. 7 , such as a microfluidic or column-based flowinstrument. The method described herein can easily be performed in aflow setup which makes the method simple to use. It will be understoodthat examples of commercially available DNA synthesisers (e.g., MerMade192E from BioAutomation or H-8 SE from K&A) may be optimised for therequired reaction conditions and used to perform the method describedherein.

In one embodiment, the method is performed on a plate or microarraysetup. For example, nucleotides may be individually addressed through aseries of microdispensing nozzles using any applicable jettingtechnology, including piezo and thermal jets. This highly parallelprocess may be used to generate hybridization microarrays and is alsoamenable to DNA fragment assembly through standard molecular biologytechniques.

In one embodiment, the method additionally comprises amplifying theresultant nucleic acid. Methods of DNA/RNA amplification are well knownin the art. For example, in a further embodiment, the amplification isperformed by polymerase chain reaction (PCR). This step has theadvantage of being able to extract and amplify the resultant nucleicacid all in one step.

The template independent nucleic acid synthesis method described hereinhas the capability to add a nucleic acid sequence of defined compositionand length to an initiator sequence. Therefore, it will be understood bypersons skilled in the art, that the method described herein may be usedas a novel way to introduce adapter sequences to a nucleic acid library.

If the initiator sequence is not one defined sequence, but instead alibrary of nucleic acid fragments (for example generated by sonicationof genomic DNA, or for example messenger RNA) then this method iscapable of de novo synthesis of ‘adapter sequences’ on every fragment.The installation of adapter sequences is an integral part of librarypreparation for next-generation library nucleic acid sequencing methods,as they contain sequence information allowing hybridisation to a flowcell/solid support and hybridisation of a sequencing primer.

Currently used methods include single-stranded ligation, however thistechnique is limited because ligation efficiency decreases strongly withincreasing fragment length. Consequently, current methods are unable toattach sequences longer than 100 nucleotides in length. Therefore, themethod described herein allows for library preparation in an improvedfashion to that which is currently possible.

Therefore, in one embodiment, an adapter sequence is added to theinitiator sequence. In a further embodiment, the initiator sequence maybe a nucleic acid from a library of nucleic acid fragments.

Kits

According to a further aspect of the invention, there is provided theuse of a kit in a method of nucleic acid synthesis, wherein said kitcomprises a TdT as defined in the first or second aspects of theinvention optionally in combination with one or more components selectedfrom: an initiator sequence, one or more 3′-blocked nucleotidetriphosphates, inorganic pyrophosphatase, such as purified, recombinantinorganic pyrophosphatase from Saccharomyces cerevisiae, and a cleavingagent; further optionally together with instructions for use of the kitin accordance with any of the methods defined herein.

Suitably a kit according to the invention may also contain one or morecomponents selected from the group: an extension solution, a washsolution and/or a cleaving solution as defined herein; optionallytogether with instructions for use of the kit in accordance with any ofthe methods defined herein.

Use of 3′-Blocked Nucleotide Triphosphates

According to a further aspect of the invention, there is provided theuse of a 3′-blocked nucleotide triphosphate in a method of templateindependent nucleic acid synthesis, wherein the 3′-blocked nucleotidetriphosphate is selected from a compound of formula (I), (II), (III) or(IV):

wherein

-   -   R¹ represents NR^(a)R^(b), wherein R^(a) and R^(b) independently        represent hydrogen or C₁₋₆ alkyl,    -   R² represents hydrogen, C₁₋₆ alkyl, C₁₋₆ alkoxy, COH or COOH.    -   X represents C₁₋₆ alkyl, NH₂, N₃ or —OR³,    -   R³ represents C₁₋₆ alkyl, CH₂N₃, NH₂ or allyl,    -   Y represents hydrogen, halogen or hydroxyl, and    -   Z represents CR⁴ or N, wherein R⁴ represents hydrogen, C₁₋₆        alkyl, C₁₋₆alkoxy, COH or COOH.

References herein to a “template independent nucleic acid synthesismethod” refer to a method of nucleic acid synthesis which does notrequire a template DNA/RNA strand, i.e. the nucleic acid can besynthesised de novo.

In one embodiment, the nucleic acid is DNA. References herein to a“template independent DNA synthesis method” refer to a method of DNAsynthesis which does not require a template DNA strand, i.e. the DNA canbe synthesised de novo. In an alternative embodiment, the nucleic acidis RNA.

It will be understood that PPP′ in the structures shown hereinrepresents a triphosphate group.

References to the term ‘C₁₋₆ alkyl’ as used herein as a group or part ofa group refers to a linear or branched saturated hydrocarbon groupcontaining from 1 to 6 carbon atoms. Examples of such groups includemethyl, ethyl, butyl, n-propyl, isopropyl and the like.

References to the term ‘C₁₋₆ alkoxy’ as used herein refer to an alkylgroup bonded to oxygen via a single bond (i.e. R—O). Such referencesinclude those with straight and branched alkyl chains containing 1 to 6carbon atoms, such as methoxy (or methyloxy), ethyloxy, n-propyloxy,iso-propyloxy, n-butyloxy and 2-methylpropyloxy.

References to the term ‘allyl’ as used herein refer to a substituentwith the structural formula RCH₂—CH═CH₂, where R is the rest of themolecule. It consists of a methyl group (—CH₂—) attached to a vinylgroup (—CH═CH₂).

References to the term ‘COOH’ or ‘CO₂H’ refer to a carboxyl group (orcarboxy) which consists of a carbonyl (C═O) and a hydroxyl (O—H) group.References to the term ‘COH’ refer to a formyl group which consists of acarbonyl (C═O) group bonded to hydrogen.

The term ‘N₃’ (drawn structurally as —N═N⁺═N⁻) refers to an azido group.

In one embodiment, R^(a) and R^(b) both represent hydrogen (i.e. R¹represents NH₂).

In an alternative embodiment, R^(a) represents hydrogen and R^(b)represents methyl (i.e. R¹ represents NHCH₃).

In one embodiment, R² represents hydrogen, methyl or methoxy. In afurther embodiment, R² represents hydrogen. In an alternativeembodiment, R² represents methyl. In a yet further alternativeembodiment, R² represents methoxy.

In one embodiment, X represents —OR³, and R³ represents C₁₋₆ alkyl,CH₂N₃, NH₂ or allyl.

In an alternative embodiment, X represents C₁₋₆ alkyl (such as methyl)or N₃.

In one embodiment, Y represents hydrogen or hydroxyl.

In one embodiment, Y represents hydrogen.

In an alternative embodiment, Y represents hydroxyl.

In an alternative embodiment, Y represents halogen, such as fluorine.

In one embodiment, Z represents N.

In an alternative embodiment, Z represents CR⁴.

In one embodiment, R⁴ represents C₁₋₆ alkyl, C₁₋₆alkoxy, COH or COOH.

In a further embodiment, R⁴ represents methoxy, COOH or COH. In a yetfurther embodiment, R⁴ represents methoxy. In an alternative embodiment,R⁴ represents COOH. In a yet further alternative embodiment, R⁴represents COH.

In one embodiment, the 3′-blocked nucleotide triphosphate is selectedfrom:

Structure Name Example number

Deoxyadenosine triphosphate E1

Deoxyguanosine triphosphate E2

Deoxythymidine triphosphate E3

Deoxycytidine triphosphate E4

2′-deoxy-uridine triphosphate E5

5-aza-2′-deoxy-cytidine- triphosphate E6

5-hydroxymethyl- deoxycytidine triphosphate E7

5-carboxy-deoxycytidine triphosphate E8

5-formyl-deoxycytidine triphosphate E9

N6-methyladenosine triphosphate E10

5-hydroxymethyl-deoxy- uridine triphosphate E11

wherein ‘X’ is as defined hereinbefore.

The following studies and protocols illustrate embodiments of themethods described herein:

Comparative Example 1: Use of Bos taurus TdT to Add 3′-IrreversiblyBlocked Nucleotide Triphosphates to a DNA Initiator

A single-stranded DNA initiator (SEQ ID NO: 7) was incubated with 15 UBos taurus TdT (Thermo Scientific), required salts (50 mM potassiumacetate, 20 mM tris acetate pH 7.9, 1 mM cobalt chloride), and3′-O-Methyl dTTP (TriLink) at 37° C. for up to one hour. The3′-irreversibly blocked nucleotide triphosphate was at a concentrationof 1 mM and the DNA initiator at 200 μM for a 1:5000 ratio to encouragenucleotide addition. The reaction was stopped with EDTA (0.5 M) atvarious intervals and the results are shown in FIG. 2(A).

The experiment was repeated with the exception that 3′-Azido dTTP wasused as the 3′-irreversibly blocked nucleotide triphosphate instead of3′-O-Methyl dTTP. The reaction was stopped with EDTA (0.5 M) at variousintervals and the results are shown in FIG. 2(B).

These studies show that the commercially available Bos taurus TdT addsirreversibly blocked nucleotides, specifically 3′-O-Methyl dTTP and3′-Azido dTTP onto a DNA initiator strand (FIG. 2 ). Furthermore, theaddition of a 3′-blocked nucleotide triphosphate to a single-strandedDNA initiator is completed to greater than 90% conversion of the nstrand to the n+1 strand.

Example 2: Use of TdT Orthologs Other than Bos Taurus TdT for ControlledTemplate-Independent DNA Synthesis

A single-stranded DNA initiator (SEQ ID NO: 7) was incubated withpurified, recombinant TdT orthologs, required salts (50 mM potassiumacetate, 20 mM tris acetate pH 7.9, 1.5 mM cobalt chloride,Saccharomyces cerevisiae inorganic pyrophosphatase), and3′-O-azidomethyl dTTP at 37° C. for 60 min. The 3′-blocked nucleotidetriphosphate was at a concentration of 1 mM and the DNA initiator at 200nM and analysed via capillary electrophoresis as shown in FIG. 3(A).Reactions were quantified after 60 min and results are shown in FIG.3(B).

The experiment was repeated with the exception that both3′-O-azidomethyl dTTP and 3′-O-azidomethyl dCTP was used as the3′-blocked nucleotide triphosphate. The reaction was stopped after 20min and analysed via capillary electrophoresis. Quantified reactions areshown in FIG. 3(C).

Bos taurus TdT only efficiently adds irreversibly blocked nucleotides,which is not useful for controlled, enzymatic single-stranded DNAsynthesis. This example demonstrates that naturally occurring TdTorthologs other than Bos taurus TdT perform significantly better atadding 3′-reversibly blocked nucleotide triphosphates. Betterperformance, which is judged by the N+1 addition rate (FIG. 3 ), resultsin longer achievable lengths and greater control of nucleic acidsequence specificity.

Example 3: Engineered TdT Orthologs Demonstrate Improved Function OverWild-Type Proteins

A single-stranded DNA initiator (SEQ ID NO: 7) was incubated with eithera purified wild-type Lepisosteus oculatus TdT or a purified, recombinantengineered form of Lepisosteus oculatus TdT (SEQ ID NO: 8), requiredsalts, cobalt chloride, Saccharomyces cerevisiae inorganicpyrophosphatase, and 3′-O-azidomethyl dTTP at 37° C. for 20 min.

The wild-type Lepisosteus oculatus TdT was outperformed by theengineered variant (SEQ ID NO: 8), as demonstrated by improved abilityto convert the initiator strand of length n to a strand of length n+1,when supplied with 3′-reversibly blocked dCTP, dGTP or dTTP.

Example 4: Use of Engineered TdT Orthologs for Template-Independent andSequence-Specific DNA Synthesis

A single-stranded DNA initiator (SEQ ID NO: 7) was incubated with apurified, recombinant engineered form of Lepisosteus oculatus TdT,required salts, cobalt chloride, Saccharomyces cerevisiae inorganicpyrophosphatase, and 3′-O-azidomethyl dTTP at 37° C. for 10 min.

Bos Taurus TdT was outperformed by an engineered variant of Lepisosteusoculatus TdT, as demonstrated by the denaturing PAGE gel in FIG. 5 .This example demonstrates an engineered form of Lepisosteus oculatus TdTincorporates 3′-reversibly blocked nucleotides (1) better than thewild-type Lepisosteus oculatus TdT, and (2) much better than Bos TaurusTdT (see FIGS. 2-5 ).

Example 5: Use of Inorganic Pyrophosphatase to Control Nucleic AcidSequence Specificity

A single-stranded DNA initiator (SEQ ID NO: 7) was incubated with Bostaurus TdT at 37° C. for 60 min under the reaction buffer shown abovewith the exception that the concentration of Saccharomyces cerevisiaeinorganic pyrophosphatase was varied. When dideoxyTTP (ddTTP) was used,the concentration of the NTP was 0.1 mM. Reactions were analysed by PAGEand are shown in FIG. 6 .

The inorganic pyrophosphatase studies with TdT demonstrate thatTdT-mediated DNA synthesis must utilise an inorganic pyrophosphatase inorder to control nucleic acid sequence specificity.

Example 6: Example DNA Synthesis Method Using TdT

1. An immobilised single-stranded DNA initiator is exposed to theextension solution, which is composed of TdT; a base-specific 3′-blockednucleotide triphosphate; inorganic pyrophosphatase (e.g., theSaccharomyces cerevisiae homolog); and any required buffers (e.g.,tris(hydroxymethyl)aminomethane (Tris), cacodylate, or any buffer with abuffering range between pH 5-10) and salts (e.g., Na⁺, K⁺, Mg²⁺, Mn²⁺,Cu²⁺, Zn²⁺, Co²⁺, etc., all with appropriate counterions, such as Cl⁻)and reacted at optimised concentrations, times and temperatures. The3′-blocked nucleotide triphosphate will contain one of the nitrogenousbases adenine, guanine, cytosine or thymine.

2. The extension mixture is then removed with wash mixture and recycled.Wash mixture is the extension mixture without TdT and the 3′-blockednucleotide triphosphate.

3. The immobilised (n+1) DNA strand is treated with cleavage mixturecomposed of an appropriate buffer, denaturant (e.g., urea, guanidiniumchloride, formamide, betaine, etc.), and cleavage agent (e.g.,tris(2-carboxyethyl)phosphine (TCEP) to de-block a 3′-O-azidomethylgroup; palladium complexes to de-block 3′-O-allyl group; or sodiumnitrite to de-block the 3′-aminoxy group). The temperature can be raisedup to 99° C. to assist in cleavage and disruption of secondarystructures. The optimal temperature depends on the cleavage agentutilised.

4. The immobilised deblocked (n+1) DNA strand is treated with washmixture to remove the cleavage mixture.

5. Cycles 1˜4 are repeated with the base-specific 3′-blocked nucleotidetriphosphate until the desired oligonucleotide sequence is achieved.

6. Once the desired sequence is achieved, polymerase chain reaction withprimers specific to the DNA product is used to directly “extract” andamplify the product.

The invention claimed is:
 1. A kit for use in a method of nucleic acidsynthesis, wherein said kit comprises a terminal deoxynucleotidyltransferase (TdT) comprising an amino acid sequence of at least 95%sequence identity to any one of SEQ ID NOS: 1 to 5 and 8 or a functionalfragment thereof having terminal deoxynucleotidyl transferase activityand comprising an N-terminal or a C-terminal truncation, in combinationwith one or more 3-blocked nucleoside triphosphates.
 2. The kit asdefined in claim 1, further comprising an initiator oligonucleotide. 3.The kit as defined in claim 2, wherein the initiator oligonucleotide isimmobilised on a solid support.
 4. The kit as defined in claim 1, whichadditionally comprises one or more components selected from the group:an extension solution, a wash solution, and/or a cleaving solution. 5.The kit as defined in claim 1, wherein the terminal deoxynucleotidyltransferase (TdT) comprises an amino acid sequence having at least 95%sequence identity to SEQ ID NO: 8 or a functional fragment thereofhaving terminal deoxynucleotidyl transferase activity, and comprising anN-terminal or a C-terminal truncation.
 6. The kit as defined in claim 1,wherein the 3′-blocked nucleoside triphosphate is blocked by either a3′-O-azidomethyl, 3′-aminoxy or 3′-O-allyl group.
 7. The kit as definedin claim 4, wherein the extension solution comprises one or morebuffers, one or more salts, and inorganic pyrophosphatase.
 8. The kit asdefined in claim 4, wherein the cleaving solution comprises a cleavingagent.
 9. The kit as defined in claim 8, wherein the cleaving agent is achemical cleaving agent.
 10. The kit as defined in claim 8, wherein thecleaving agent is selected from: tris(2-carboxyethyl)phosphine (TCEP), apalladium complex, or sodium nitrite.
 11. The kit as defined in claim 4,wherein the cleaving solution comprises a denaturant selected from urea,guanidinium chloride, formamide or betaine, and one or more buffers.